Package picard.sam
Class CompareSAMs
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.sam.CompareSAMs
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@DocumentedFeature public class CompareSAMs extends CommandLineProgram
Rudimentary SAM comparer. Compares headers, and if headers are compatible enough, compares SAMRecords, looking only at basic alignment info. Summarizes the number of alignments that match, mismatch, are missing, etc.
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Field Summary
Fields Modifier and Type Field Description File
OUTPUT
List<File>
SAM_FILES
SAMComparisonArgumentCollection
samComparisonArgumentCollection
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description CompareSAMs()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.-
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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SAM_FILES
@PositionalArguments(doc="Exactly two input SAM/BAM/CRAM files to compare to one another.", minElements=2, maxElements=2) public List<File> SAM_FILES
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OUTPUT
@Argument(shortName="O", doc="Output file to write comparison results to.", optional=true) public File OUTPUT
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samComparisonArgumentCollection
@ArgumentCollection public SAMComparisonArgumentCollection samComparisonArgumentCollection
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Method Detail
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doWork
protected int doWork()
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
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